Notes
- raw metrics from Cell Ranger (CR) count runs
- CR 6.1.1 (Gencode 40, ensembl v106)
Samples table
- include percentage of swapped counts from swappedDrops() with
different min.frac values
Metrics table
- compare some metrics from CR counts output stored in
metrics_summary.csv of each sample
scFlow
- use cells called from Cell Ranger
SessionInfo
## ─ Session info ───────────────────────────────────────────────────────────────
## setting value
## version R version 4.2.0 (2022-04-22)
## os macOS Big Sur/Monterey 10.16
## system x86_64, darwin17.0
## ui X11
## language (EN)
## collate en_GB.UTF-8
## ctype en_GB.UTF-8
## tz Europe/London
## date 2022-06-15
## pandoc 2.17.1.1 @ /Applications/RStudio.app/Contents/MacOS/quarto/bin/ (via rmarkdown)
##
## ─ Packages ───────────────────────────────────────────────────────────────────
## package * version date (UTC) lib source
## abind 1.4-5 2016-07-21 [1] CRAN (R 4.2.0)
## assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.2.0)
## backports 1.4.1 2021-12-13 [1] CRAN (R 4.2.0)
## beachmat 2.12.0 2022-04-26 [1] Bioconductor
## beeswarm 0.4.0 2021-06-01 [1] CRAN (R 4.2.0)
## Biobase * 2.56.0 2022-04-26 [1] Bioconductor
## BiocGenerics * 0.42.0 2022-04-26 [1] Bioconductor
## BiocNeighbors 1.14.0 2022-04-26 [1] Bioconductor
## BiocParallel 1.30.3 2022-06-05 [1] Bioconductor
## BiocSingular 1.12.0 2022-04-26 [1] Bioconductor
## bitops 1.0-7 2021-04-24 [1] CRAN (R 4.2.0)
## brio 1.1.3 2021-11-30 [1] CRAN (R 4.2.0)
## broom 0.8.0 2022-04-13 [1] CRAN (R 4.2.0)
## bslib 0.3.1 2021-10-06 [1] CRAN (R 4.2.0)
## cachem 1.0.6 2021-08-19 [1] CRAN (R 4.2.0)
## callr 3.7.0 2021-04-20 [1] CRAN (R 4.2.0)
## car 3.0-13 2022-05-02 [1] CRAN (R 4.2.0)
## carData 3.0-5 2022-01-06 [1] CRAN (R 4.2.0)
## cli 3.3.0 2022-04-25 [1] CRAN (R 4.2.0)
## codetools 0.2-18 2020-11-04 [1] CRAN (R 4.2.0)
## colorspace 2.0-3 2022-02-21 [1] CRAN (R 4.2.0)
## crayon 1.5.1 2022-03-26 [1] CRAN (R 4.2.0)
## crosstalk 1.2.0 2021-11-04 [1] CRAN (R 4.2.0)
## data.table * 1.14.2 2021-09-27 [1] CRAN (R 4.2.0)
## DBI 1.1.2 2021-12-20 [1] CRAN (R 4.2.0)
## DelayedArray 0.22.0 2022-04-26 [1] Bioconductor
## DelayedMatrixStats 1.18.0 2022-04-26 [1] Bioconductor
## desc 1.4.1 2022-03-06 [1] CRAN (R 4.2.0)
## devtools 2.4.3 2021-11-30 [1] CRAN (R 4.2.0)
## digest 0.6.29 2021-12-01 [1] CRAN (R 4.2.0)
## dplyr 1.0.9 2022-04-28 [1] CRAN (R 4.2.0)
## DT * 0.23 2022-05-10 [1] CRAN (R 4.2.0)
## ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.2.0)
## evaluate 0.15 2022-02-18 [1] CRAN (R 4.2.0)
## fansi 1.0.3 2022-03-24 [1] CRAN (R 4.2.0)
## fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.2.0)
## fs 1.5.2 2021-12-08 [1] CRAN (R 4.2.0)
## generics 0.1.2 2022-01-31 [1] CRAN (R 4.2.0)
## GenomeInfoDb * 1.32.2 2022-05-15 [1] Bioconductor
## GenomeInfoDbData 1.2.8 2022-05-06 [1] Bioconductor
## GenomicRanges * 1.48.0 2022-04-26 [1] Bioconductor
## ggbeeswarm 0.6.0 2017-08-07 [1] CRAN (R 4.2.0)
## ggplot2 * 3.3.6 2022-05-03 [1] CRAN (R 4.2.0)
## ggpubr * 0.4.0 2020-06-27 [1] CRAN (R 4.2.0)
## ggrepel 0.9.1 2021-01-15 [1] CRAN (R 4.2.0)
## ggsignif 0.6.3 2021-09-09 [1] CRAN (R 4.2.0)
## glue 1.6.2 2022-02-24 [1] CRAN (R 4.2.0)
## gridExtra 2.3 2017-09-09 [1] CRAN (R 4.2.0)
## gtable 0.3.0 2019-03-25 [1] CRAN (R 4.2.0)
## htmltools 0.5.2 2021-08-25 [1] CRAN (R 4.2.0)
## htmlwidgets 1.5.4 2021-09-08 [1] CRAN (R 4.2.0)
## IRanges * 2.30.0 2022-04-26 [1] Bioconductor
## irlba 2.3.5 2021-12-06 [1] CRAN (R 4.2.0)
## jquerylib 0.1.4 2021-04-26 [1] CRAN (R 4.2.0)
## jsonlite 1.8.0 2022-02-22 [1] CRAN (R 4.2.0)
## knitr * 1.39 2022-04-26 [1] CRAN (R 4.2.0)
## lattice 0.20-45 2021-09-22 [1] CRAN (R 4.2.0)
## lifecycle 1.0.1 2021-09-24 [1] CRAN (R 4.2.0)
## magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.2.0)
## Matrix 1.4-1 2022-03-23 [1] CRAN (R 4.2.0)
## MatrixGenerics * 1.8.0 2022-04-26 [1] Bioconductor
## matrixStats * 0.62.0 2022-04-19 [1] CRAN (R 4.2.0)
## memoise 2.0.1 2021-11-26 [1] CRAN (R 4.2.0)
## munsell 0.5.0 2018-06-12 [1] CRAN (R 4.2.0)
## pillar 1.7.0 2022-02-01 [1] CRAN (R 4.2.0)
## pkgbuild 1.3.1 2021-12-20 [1] CRAN (R 4.2.0)
## pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.2.0)
## pkgload 1.2.4 2021-11-30 [1] CRAN (R 4.2.0)
## prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.2.0)
## processx 3.6.0 2022-06-10 [1] CRAN (R 4.2.0)
## ps 1.7.0 2022-04-23 [1] CRAN (R 4.2.0)
## purrr 0.3.4 2020-04-17 [1] CRAN (R 4.2.0)
## R6 2.5.1 2021-08-19 [1] CRAN (R 4.2.0)
## Rcpp 1.0.8.3 2022-03-17 [1] CRAN (R 4.2.0)
## RCurl 1.98-1.7 2022-06-09 [1] CRAN (R 4.2.0)
## remotes 2.4.2 2021-11-30 [1] CRAN (R 4.2.0)
## rlang 1.0.2 2022-03-04 [1] CRAN (R 4.2.0)
## rmarkdown 2.14 2022-04-25 [1] CRAN (R 4.2.0)
## rprojroot 2.0.3 2022-04-02 [1] CRAN (R 4.2.0)
## rstatix 0.7.0 2021-02-13 [1] CRAN (R 4.2.0)
## rstudioapi 0.13 2020-11-12 [1] CRAN (R 4.2.0)
## rsvd 1.0.5 2021-04-16 [1] CRAN (R 4.2.0)
## S4Vectors * 0.34.0 2022-04-26 [1] Bioconductor
## sass 0.4.1 2022-03-23 [1] CRAN (R 4.2.0)
## ScaledMatrix 1.4.0 2022-04-26 [1] Bioconductor
## scales 1.2.0 2022-04-13 [1] CRAN (R 4.2.0)
## scater * 1.24.0 2022-04-26 [1] Bioconductor
## scuttle * 1.6.2 2022-05-17 [1] Bioconductor
## sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.2.0)
## SingleCellExperiment * 1.18.0 2022-04-26 [1] Bioconductor
## sparseMatrixStats 1.8.0 2022-04-26 [1] Bioconductor
## stringi 1.7.6 2021-11-29 [1] CRAN (R 4.2.0)
## stringr 1.4.0 2019-02-10 [1] CRAN (R 4.2.0)
## SummarizedExperiment * 1.26.1 2022-05-01 [1] Bioconductor
## testthat 3.1.4 2022-04-26 [1] CRAN (R 4.2.0)
## tibble 3.1.7 2022-05-03 [1] CRAN (R 4.2.0)
## tidyr 1.2.0 2022-02-01 [1] CRAN (R 4.2.0)
## tidyselect 1.1.2 2022-02-21 [1] CRAN (R 4.2.0)
## usethis 2.1.6 2022-05-25 [1] CRAN (R 4.2.0)
## utf8 1.2.2 2021-07-24 [1] CRAN (R 4.2.0)
## vctrs 0.4.1 2022-04-13 [1] CRAN (R 4.2.0)
## vipor 0.4.5 2017-03-22 [1] CRAN (R 4.2.0)
## viridis 0.6.2 2021-10-13 [1] CRAN (R 4.2.0)
## viridisLite 0.4.0 2021-04-13 [1] CRAN (R 4.2.0)
## withr 2.5.0 2022-03-03 [1] CRAN (R 4.2.0)
## xfun 0.31 2022-05-10 [1] CRAN (R 4.2.0)
## XVector 0.36.0 2022-04-26 [1] Bioconductor
## yaml 2.3.5 2022-02-21 [1] CRAN (R 4.2.0)
## zlibbioc 1.42.0 2022-04-26 [1] Bioconductor
##
## [1] /Library/Frameworks/R.framework/Versions/4.2/Resources/library
##
## ──────────────────────────────────────────────────────────────────────────────